/*
 *  Copyright (c) 2010 Mathew Hall.
 *  All rights reserved.
 * 
 *  Redistribution and use in source and binary forms, with or
 *  without modification, are permitted provided that the following conditions
 *  are met:
 * 
 *  Redistributions of source code must retain the above copyright
 *  notice, this list of conditions and the following disclaimer.
 *  Redistributions in binary form must reproduce the above
 *  copyright notice, this list of conditions and the following
 *  disclaimer in the documentation and/or other materials provided
 *  with the distribution.
 *  Neither the name of the <ORGANIZATION> nor the names of its
 *  contributors may be used to endorse or promote products derived
 *  from this software without specific prior written permission.
 * 
 *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
 *  CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
 *  INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 *  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 *  DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 *  CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 *  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
 *  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 *  LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
 *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 *  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
 *  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
 *  EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */
package search.searchtechniques;



import org.jgap.Chromosome;
import org.jgap.Configuration;
import org.jgap.Genotype;
import org.jgap.IChromosome;
import org.jgap.InvalidConfigurationException;
import org.jgap.impl.DefaultConfiguration;
import primitives.cluster.ClusterHead;
import search.fitnessfunctions.util.TreeTranslator;


/**
 * 
 * @author Mathew Hall
 */
public class GeneticAlgorithmSearch extends Search {
        Configuration gaConf;
        Genotype genotype;
        IChromosome fittest;
        double fitness;
        
        public GeneticAlgorithmSearch(){
        
        }
        
    @Override
        protected void setup() throws InvalidConfigurationException{
                gaConf = new DefaultConfiguration();
		gaConf.setPreservFittestIndividual(true);

                
		GeneFactory gf = new GeneFactory(geneType, in.getSize());
		
		IChromosome sampleChromosome = new Chromosome(gaConf, gf.getInstance(gaConf),
					chromesize);
		
                
		gaConf.setSampleChromosome(sampleChromosome);
		gaConf.setPopulationSize(popsize);
		
		gaConf.setFitnessFunction(ff);
		
                genotype = Genotype.randomInitialGenotype(gaConf);
                

        }
    
        public double iteration(){
            for(IChromosome ic : genotype.getPopulation().getChromosomes()){
                            ic.setApplicationData(geneType);
                        }
            genotype.evolve();
            fittest = genotype.getFittestChromosome();
            fitness = fittest.getFitnessValue();
            
            return fitness;
        }
        
        public ClusterHead getClustering(){
            return TreeTranslator.getTree(fittest, in);
        }
        
        public double getFitness(){
            return fitness;
        }
}
